Contig-U06553-1
Contig ID Contig-U06553-1
Contig update 2002. 9.13
Contig sequence
>Contig-U06553-1 (Contig-U06553-1Q) /CSM_Contig/Contig-U06553-1Q.Seq.d
AAAAANNNNAAAAANNGGGGNNNGGGNCCCCCCCNNNGGGNNANAAAAGG
GGNNAAAAAAAAAAANNTTTTTTNGNNTTNNCCAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAATCTACAATAACCAGAGTAAAACTTTATTAC
ATAAAAGATTTGTAAAATTTTGTTTAAAGAATAGTTTATTACCAAAATCG
GCAATCATTATAAAAGAAAATTAATTC

Gap no gap
Contig length 227
Chromosome number (1..6, M) 2
Chromosome length 8467578
Start point 1236298
End point 1236442
Strand (PLUS/MINUS) PLUS
Number of clones 1
Number of EST 1
Link to clone list U06553
List of clone(s)

est1=VSD485Z,1,228
Translated Amino Acid sequence
KXXKXGXGXPPXGXKRGXKKKXFXXXXKKKKKKKKKKKKIYNNQSKTLLHKRFVKFCLKN
SLLPKSAIIIKEN*f


Translated Amino Acid sequence (All Frames)
Frame A:
kxxkxxgxgppxxxxkgxkkkxxfxxxpkkkkkkkkkkkkstitrvklyyikdl*nfv*r
ivyyqnrqsl*kkin


Frame B:
kxxkxgxxxppxgxxkgxkkkxffxxxqkkkkkkkkkkknlq*pe*nfit*kickilfke
*fitkignhykrkli


Frame C:
KXXKXGXGXPPXGXKRGXKKKXFXXXXKKKKKKKKKKKKIYNNQSKTLLHKRFVKFCLKN
SLLPKSAIIIKEN*f


own update 2004. 6.10
Homology vs CSM-cDNA
Query= Contig-U06553-1 (Contig-U06553-1Q)
/CSM_Contig/Contig-U06553-1Q.Seq.d
(227 letters)

Database: CSM
6905 sequences; 5,674,871 total letters


Score E
Sequences producing significant alignments: (bits) Value

Contig-U06553-1 (Contig-U06553-1Q) /CSM_Contig/Conti... 212 1e-55
Contig-U13551-1 (Contig-U13551-1Q) /CSM_Contig/Conti... 36 0.015
Contig-U12249-1 (Contig-U12249-1Q) /CSM_Contig/Conti... 32 0.24
Contig-U10975-1 (Contig-U10975-1Q) /CSM_Contig/Conti... 32 0.24
Contig-U10719-1 (Contig-U10719-1Q) /CSM_Contig/Conti... 32 0.24
Contig-U14428-1 (Contig-U14428-1Q) /CSM_Contig/Conti... 30 0.94
Contig-U13589-1 (Contig-U13589-1Q) /CSM_Contig/Conti... 30 0.94
Contig-U13554-1 (Contig-U13554-1Q) /CSM_Contig/Conti... 30 0.94
Contig-U14126-1 (Contig-U14126-1Q) /CSM_Contig/Conti... 28 3.7

>Contig-U06553-1 (Contig-U06553-1Q) /CSM_Contig/Contig-U06553-1Q.Seq.d
Length = 227

Score = 212 bits (107), Expect = 1e-55
Identities = 107/107 (100%)
Strand = Plus / Plus


Query: 121 tctacaataaccagagtaaaactttattacataaaagatttgtaaaattttgtttaaaga 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 121 tctacaataaccagagtaaaactttattacataaaagatttgtaaaattttgtttaaaga 180


Query: 181 atagtttattaccaaaatcggcaatcattataaaagaaaattaattc 227
|||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 181 atagtttattaccaaaatcggcaatcattataaaagaaaattaattc 227


>Contig-U13551-1 (Contig-U13551-1Q) /CSM_Contig/Contig-U13551-1Q.Seq.d
Length = 1117

Score = 36.2 bits (18), Expect = 0.015
Identities = 18/18 (100%)
Strand = Plus / Minus


Query: 210 ataaaagaaaattaattc 227
||||||||||||||||||
Sbjct: 548 ataaaagaaaattaattc 531


>Contig-U12249-1 (Contig-U12249-1Q) /CSM_Contig/Contig-U12249-1Q.Seq.d
Length = 2111

Score = 32.2 bits (16), Expect = 0.24
Identities = 16/16 (100%)
Strand = Plus / Plus


Query: 173 tttaaagaatagttta 188
||||||||||||||||
Sbjct: 1192 tttaaagaatagttta 1207


Database: CSM
Posted date: Jun 9, 2004 7:35 PM
Number of letters in database: 5,674,871
Number of sequences in database: 6905

Lambda K H
1.37 0.711 1.31

Gapped
Lambda K H
1.37 0.711 1.31


Matrix: blastn matrix:1 -3
Gap Penalties: Existence: 5, Extension: 2
Number of Hits to DB: 2362
Number of Sequences: 6905
Number of extensions: 2362
Number of successful extensions: 747
Number of sequences better than 10.0: 77
length of query: 227
length of database: 5,674,871
effective HSP length: 15
effective length of query: 212
effective length of database: 5,571,296
effective search space: 1181114752
effective search space used: 1181114752
T: 0
A: 40
X1: 6 (11.9 bits)
X2: 15 (29.7 bits)
S1: 12 (24.3 bits)
S2: 14 (28.2 bits)
dna update 2008.11. 9
Homology vs DNA
Query= Contig-U06553-1 (Contig-U06553-1Q) /CSM_Contig/Contig-U06553-1Q.Seq.d
(227 letters)

Database: ddbj_A
92,845,959 sequences; 95,242,211,685 total letters

Searching..................................................done

Score E
Sequences producing significant alignments: (bits) Value N

(AC116920) Dictyostelium discoideum chromosome 2 map 4415041... 212 4e-51 1
(AU264115) Dictyostelium discoideum vegetative cDNA clone:VS... 212 4e-51 1
(AP009280) Solanum lycopersicum genomic DNA, chromosome 8, c... 40 0.12 4
(AJ828646) Helianthus annuus EST, clone HaCotR010D06. 34 0.38 2
(CU657954) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f... 46 0.51 1
(AY915911) Schistosoma japonicum splicing factor 4 mRNA, com... 46 0.51 1
(BU766692) SJEAIH03 SJE Schistosoma japonicum cDNA similar t... 46 0.51 1
(EK094683) 1092962026858 Global-Ocean-Sampling_GS-31-01-01-1... 34 1.4 2
(BH663698) BOHVD35TF BO_2_3_KB Brassica oleracea genomic clo... 34 1.4 2
(EK108528) 1092963077112 Global-Ocean-Sampling_GS-31-01-01-1... 34 1.4 2
(BH532868) BOGDF29TR BOGD Brassica oleracea genomic clone BO... 34 1.4 2
(EV590925) Dmel_neb_009584_0344_3069 D. melanogaster - 454 s... 32 1.4 3
(EY024125) JGI_CAFF436.rev CAFF Acropora palmata 15 day old ... 34 1.5 2
(CU571160) Zebrafish DNA sequence from clone CH73-160J1 in l... 44 2.0 1
(AC190525) Pan troglodytes BAC clone CH251-257H9 from chromo... 44 2.0 1
(AC095067) Homo sapiens BAC clone RP11-655F21 from 7, comple... 44 2.0 1
(AC126602) Ciona savignyi clone -4791857N6, *** SEQUENCING I... 44 2.0 1
(AC211982) Pan troglodytes chromosome 7 clone CH251-376H21, ... 44 2.0 1
(AC211789) Pan troglodytes chromosome 7 clone CH251-73F4, **... 44 2.0 1
(AC018998) Homo sapiens clone RP11-21H20, WORKING DRAFT SEQU... 44 2.0 1
(EJ543900) 1092955417751 Global-Ocean-Sampling_GS-29-01-01-1... 44 2.0 1
(DU482302) 1098415966513 CHORI-243 Ovis aries genomic clone ... 44 2.0 1
(DE209492) Branchiostoma floridae DNA, clone: CH302-098_K05_... 44 2.0 1
(AC224054) Bos taurus clone CH240-451E1, WORKING DRAFT SEQUE... 34 2.3 3
(CU207209) Medicago truncatula chromosome 5 clone mte1-84c7,... 40 3.2 3
(CR925809) Zebrafish DNA sequence from clone DKEYP-114A1 in ... 42 3.2 5
(BS000563) Pan troglodytes chromosome Y clone:PTB-623C04, co... 32 3.7 4
(AC168330) Strongylocentrotus purpuratus clone R3-58P5, WORK... 32 3.8 2
(AC092097) Homo sapiens chromosome UNK clone RP11-376A21, WO... 34 3.8 2
(AC144632) Mus musculus BAC clone RP23-106G16 from chromosom... 30 3.8 2
(BX005113) Zebrafish DNA sequence from clone CH211-203B20 in... 34 3.8 2
(AC126028) Mus musculus BAC clone RP24-542M6 from chromosome... 30 3.9 2
(AC141529) Rattus norvegicus clone CH230-516M9, WORKING DRAF... 34 3.9 2
(CS789996) Sequence 1252 from Patent WO2005031001. 30 3.9 2
(AC142368) Rattus norvegicus clone CH230-505G4, WORKING DRAF... 34 3.9 2
(AC005078) Homo sapiens BAC clone CTA-252K19 from 7, complet... 34 4.1 2
(AP009269) Solanum lycopersicum genomic DNA, chromosome 8, c... 40 4.3 3
(DU877736) 279002 Tomato HindIII BAC Library Solanum lycoper... 34 5.1 2
(CZ934123) 251575 Tomato EcoRI BAC Library Solanum lycopersi... 32 5.1 2
(FH493702) CHO_OF4610xo01f1.ab1 CHO_OF4 Nicotiana tabacum ge... 32 5.3 2
(DT199506) JGI_CAAS7063.rev CAAS Pimephales promelas brain 7... 40 5.3 2
(ES611758) MTGland_A011_2007-05-04/MTGlandA011_F03_011_1 Med... 32 5.3 2
(BQ140883) NF050B03PH1F1029 Phoma-infected Medicago truncatu... 32 5.6 2
(FH543855) CHO_OF4749xk06r1.ab1 CHO_OF4 Nicotiana tabacum ge... 40 5.6 2
(FH258780) CHO_OF3365xk18r1.ab1 CHO_OF3 Nicotiana tabacum ge... 40 5.7 2
(AC142319) Pan troglodytes BAC clone RP43-57F23 from chromos... 32 6.1 4
(AC218439) Bos taurus clone CH240-269B12, WORKING DRAFT SEQU... 34 6.3 4
(AC147672) Pan troglodytes BAC clone CH251-58K21 from chromo... 32 6.6 4
(BS000537) Pan troglodytes chromosome Y clone:PTB-100K18, co... 32 7.3 4
(CR384053) Zebrafish DNA sequence from clone DKEY-207B21 in ... 42 7.9 1
(BX890619) Zebrafish DNA sequence from clone CH211-288M1. 42 7.9 1
(BX005339) Zebrafish DNA sequence from clone DKEY-71C4 in li... 42 7.9 1
(BX004988) Zebrafish DNA sequence from clone CH211-79C4 in l... 42 7.9 1
(AL627263) Zebrafish DNA sequence from clone RP71-1L9 in lin... 42 7.9 1
(AC191859) Rhesus Macaque BAC CH250-378O7 () complete seque... 42 7.9 1
(CR382125) Kluyveromyces lactis strain NRRL Y-1140 chromosom... 42 7.9 1
(AC174344) Medicago truncatula clone mth2-167b8, complete se... 42 7.9 1
(AC165431) Medicago truncatula clone mth2-117b21, complete s... 42 7.9 1
(AR544957) Sequence 88 from patent US 6747137. 42 7.9 1
(AE014134) Drosophila melanogaster chromosome 2L, complete s... 42 7.9 1
(AC093045) Drosophila melanogaster, chromosome 2L, region 29... 42 7.9 1
(AC009523) Drosophila melanogaster, chromosome 2L, region 29... 42 7.9 1
(AC005417) Drosophila melanogaster, chromosome 2L, region 29... 42 7.9 1
(AL136136) Human DNA sequence from clone RP11-141E20 on chro... 42 7.9 1
(AC162253) Bos taurus clone CH240-109E19, WORKING DRAFT SEQU... 42 7.9 1
(AC161769) Bos taurus clone CH240-109C4, WORKING DRAFT SEQUE... 42 7.9 1
(AC161691) Bos taurus clone CH240-107N7, WORKING DRAFT SEQUE... 42 7.9 1
(AC160450) Bos taurus clone CH240-81G3, WORKING DRAFT SEQUEN... 42 7.9 1
(AC159753) Bos taurus clone CH240-81D13, WORKING DRAFT SEQUE... 42 7.9 1
(AC155086) Bos taurus clone CH240-38H19, WORKING DRAFT SEQUE... 42 7.9 1
(AC155077) Bos taurus clone CH240-35K10, WORKING DRAFT SEQUE... 42 7.9 1
(AC153705) Bos taurus clone CH240-24D5, WORKING DRAFT SEQUEN... 42 7.9 1
(AC153036) Bos taurus clone CH240-22M13, WORKING DRAFT SEQUE... 42 7.9 1
(AC152736) Bos taurus clone CH240-15C4, WORKING DRAFT SEQUEN... 42 7.9 1
(AC152645) Bos taurus clone CH240-16J22, WORKING DRAFT SEQUE... 42 7.9 1
(AC152627) Bos taurus clone CH240-6H4, WORKING DRAFT SEQUENC... 42 7.9 1
(CU651574) Zebrafish DNA sequence *** SEQUENCING IN PROGRESS... 42 7.9 1
(AC230804) Bos taurus clone CH240-498N17, WORKING DRAFT SEQU... 42 7.9 1
(AC230652) Bos taurus clone CH240-502I1, WORKING DRAFT SEQUE... 42 7.9 1
(AC230613) Bos taurus clone CH240-503P18, WORKING DRAFT SEQU... 42 7.9 1
(AC230352) Bos taurus clone CH240-511H22, WORKING DRAFT SEQU... 42 7.9 1
(AC222012) Bos taurus clone CH240-374K17, WORKING DRAFT SEQU... 42 7.9 1
(AC221414) Bos taurus clone CH240-406J7, WORKING DRAFT SEQUE... 42 7.9 1
(AC221325) Bos taurus clone CH240-403K22, WORKING DRAFT SEQU... 42 7.9 1
(AC220473) Bos taurus clone CH240-357D17, WORKING DRAFT SEQU... 42 7.9 1
(AC218649) Bos taurus clone CH240-298J15, WORKING DRAFT SEQU... 42 7.9 1
(AC218208) Bos taurus clone CH240-291F7, WORKING DRAFT SEQUE... 42 7.9 1
(AC213387) Zea mays chromosome 4 clone CH201-56A22; ZMMBBc00... 42 7.9 1
(AC207534) Zea mays chromosome 5 clone ZMMBBb-291N5; ZMMBBb0... 42 7.9 1
(AC199547) Zea mays chromosome 4 clone CH201-456M14; ZMMBBc0... 42 7.9 1
(AC192210) Zea mays chromosome 3 clone CH201-347B23; ZMMBBc0... 42 7.9 1
(AC190932) Zea mays chromosome 5 clone CH201-139B10; ZMMBBc0... 42 7.9 1
(AC184487) Strongylocentrotus purpuratus clone R3-1003B3, WO... 42 7.9 1
(AC183913) Zea mays chromosome 3 clone CH201-291H7; ZMMBBc02... 42 7.9 1
(AC182963) Bos taurus clone CH240-221E15, WORKING DRAFT SEQU... 42 7.9 1
(AC178164) Strongylocentrotus purpuratus clone R3-3081J11, W... 42 7.9 1
(AC175191) Bos taurus clone CH240-147G7, *** SEQUENCING IN P... 42 7.9 1
(AC174576) Bos taurus clone CH240-414A9, WORKING DRAFT SEQUE... 42 7.9 1
(AC174197) Bos taurus clone CH240-304G15, WORKING DRAFT SEQU... 42 7.9 1
(AC173009) Bos taurus clone CH240-197F18, WORKING DRAFT SEQU... 42 7.9 1

>(AC116920) Dictyostelium discoideum chromosome 2 map
4415041-4520361 strain AX4, complete sequence.
Length = 105320

Score = 212 bits (107), Expect = 4e-51
Identities = 107/107 (100%)
Strand = Plus / Plus


Query: 121 tctacaataaccagagtaaaactttattacataaaagatttgtaaaattttgtttaaaga 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 342 tctacaataaccagagtaaaactttattacataaaagatttgtaaaattttgtttaaaga 401


Query: 181 atagtttattaccaaaatcggcaatcattataaaagaaaattaattc 227
|||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 402 atagtttattaccaaaatcggcaatcattataaaagaaaattaattc 448

Lambda K H
1.37 0.711 1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 177,740,469
Number of extensions: 11904060
Number of successful extensions: 3580526
Number of sequences better than 10.0: 123
Length of query: 227
Length of database: 95,242,211,685
Length adjustment: 23
Effective length of query: 204
Effective length of database: 93,106,754,628
Effective search space: 18993777944112
Effective search space used: 18993777944112
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)

protein update 2009. 6.22
Homology vs Protein
Query= Contig-U06553-1 (Contig-U06553-1Q) /CSM_Contig/Contig-U06553-1Q.Seq.d
(227 letters)

Database: nrp_A
3,204,285 sequences; 1,040,966,779 total letters

Searching..................................................done

***** No hits found ******

Lambda K H
0.318 0.134 0.401

Gapped
Lambda K H
0.267 0.0410 0.140

Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 3204285
Number of Hits to DB: 241,058,184
Number of extensions: 3785412
Number of successful extensions: 2866
Number of sequences better than 10.0: 0
Number of HSP's gapped: 2862
Number of HSP's successfully gapped: 0
Length of query: 75
Length of database: 1,040,966,779
Length adjustment: 46
Effective length of query: 29
Effective length of database: 893,569,669
Effective search space: 25913520401
Effective search space used: 25913520401
Neighboring words threshold: 12
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 27 (15.0 bits)

PSORT

psg: 0.78 gvh: 0.30 alm: 0.44 top: 0.53 tms: 0.00 mit: 0.32 mip: 0.00
nuc: 0.90 erl: 0.00 erm: 0.20 pox: 0.00 px2: 0.00 vac: 0.00 rnp: 0.00
act: 0.00 caa: 0.00 yqr: 0.00 tyr: 0.00 leu: 0.00 gpi: 0.00 myr: 0.00
dna: 0.00 rib: 0.00 bac: 0.00 m1a: 0.00 m1b: 0.00 m2 : 0.00 mNt: 0.00
m3a: 0.00 m3b: 0.00 m_ : 1.00

84.0 %: nuclear
4.0 %: cytoskeletal
4.0 %: mitochondrial
4.0 %: plasma membrane
4.0 %: cytoplasmic

>> prediction for Contig-U06553-1 is nuc

VS (DIR, S) 1
VH (FL, L) 0
VF (FL, S) 0
AH (FL, L) 0
AF (FL, S) 0
SL (DIR, L) 0
SS (DIR, S) 0
SH (FL, L) 0
SF (FL, S) 0
CH (FL, L) 0
CF (FL, S) 0
FCL (DIR, L) 0
FC (DIR, S) 0
FC-IC (SUB) 0